diff --git a/frags/FindRecombinationsAmongGenomes.py b/frags/FindRecombinationsAmongGenomes.py
index eb0cdcdfc703e7d8c7b0d220941bc6d8b86da9f8..1cc88d845b1a8d700f861b81480b91db5fcacef2 100644
--- a/frags/FindRecombinationsAmongGenomes.py
+++ b/frags/FindRecombinationsAmongGenomes.py
@@ -15,7 +15,7 @@ import subprocess
from frags import core
-__version_info__ = ('0', '1', '4')
+__version_info__ = ('0', '1', '5')
__version__ = '.'.join(__version_info__)
__revision_date__ = "2020-12-17"
__author__ = "Nicolas Maillet"
@@ -40,8 +40,8 @@ def create_parser():
"genomes) and potential "\
"breakpoints (inserts "\
"between fragments). "\
- "Optionally, breakpoints can "\
- "then be Blasted again the "\
+ "Optionally, breakpoints can"\
+ " then be Blasted again the "\
"host genome, if provided.")
parser.add_argument("-i", "--inputfiles", type=str, nargs='+',
diff --git a/frags/core.py b/frags/core.py
index 90bc8ce72eae6eaf24a91382d9bed01598e580be..d3556b56736c9413fc9875bdaee8353999eab323 100644
--- a/frags/core.py
+++ b/frags/core.py
@@ -162,9 +162,9 @@ def next_read(file, offset_start, offset_end):
beg_line_offset = in_file.tell()
# Not a valid file
else:
- print("File error: enable to understand type of file {} "\
- "({})".format(file, first_line[0]))
- sys.exit(1)
+ # Stop the generator with the error to show
+ raise ValueError("File error: enable to understand type of file "\
+ "{} ({})".format(file, first_line[0]))
def build_graph(ref, k):
""" Index each k-mers of a genome
@@ -254,37 +254,39 @@ def get_recombinations(offset_start, offset_end, file, k, gap, graph1, graph2=No
"""
# Resulting Reads of current offset range
all_queries = []
+ try:
+ # Query each read, one by one, in the offset range
+ for header, sequence in next_read(file, offset_start, offset_end):
+ # Construct the Read
+ query = read.Read(header, sequence)
- # Query each read, one by one, in the offset range
- for header, sequence in next_read(file, offset_start, offset_end):
- # Construct the Read
- query = read.Read(header, sequence)
-
- # Find hits for this query
- hits = find_hits(graph1, query.sequence)
- # Transforms hits to matches
- query.get_matches(hits, gap, k, 0, 1)
- # Find hits for this query (Rev comp)
- hits_rc = find_hits(graph1, reverse_complement(query.sequence))
- # Transforms hits to matches
- query.get_matches(hits_rc, gap, k, 1, 1)
-
- # Two ref files
- if graph2:
# Find hits for this query
- hits = find_hits(graph2, query.sequence)
+ hits = find_hits(graph1, query.sequence)
# Transforms hits to matches
- query.get_matches(hits, gap, k, 0, 2)
+ query.get_matches(hits, gap, k, 0, 1)
# Find hits for this query (Rev comp)
- hits_rc = find_hits(graph2,reverse_complement(query.sequence))
+ hits_rc = find_hits(graph1, reverse_complement(query.sequence))
# Transforms hits to matches
- query.get_matches(hits_rc, gap, k, 1, 2)
-
- # Create the breakpoints
- query.get_breakpoints()
-
- # Add this query to the result
- all_queries.append(query)
+ query.get_matches(hits_rc, gap, k, 1, 1)
+
+ # Two ref files
+ if graph2:
+ # Find hits for this query
+ hits = find_hits(graph2, query.sequence)
+ # Transforms hits to matches
+ query.get_matches(hits, gap, k, 0, 2)
+ # Find hits for this query (Rev comp)
+ hits_rc = find_hits(graph2,reverse_complement(query.sequence))
+ # Transforms hits to matches
+ query.get_matches(hits_rc, gap, k, 1, 2)
+
+ # Create the breakpoints
+ query.get_breakpoints()
+
+ # Add this query to the result
+ all_queries.append(query)
+ except ValueError as exc:
+ raise exc
# Add the global result into the queue
return all_queries
@@ -311,26 +313,32 @@ def get_all_queries(file, nb_proc, k, gap, graph1, graph2=None):
chunk_size = total_size // nb_proc
# Starting offset
offset_start = 0
- # Create the pool of process
- pool = Pool()
- # Partial function to fix all but firsts arguments
- prod_recomb=partial(get_recombinations, file=file, k=k, gap=gap,
- graph1=graph1, graph2=graph2)
- # All tuples of offset_start, offset_end
- all_offsets = []
- # For each thread/chunk
- for _ in range(nb_proc - 1):
- # Compute the ending offset for this chunk
- offset_end = offset_start + chunk_size
- # Add this couple of start/end
- all_offsets.append((offset_start, offset_end))
- # Next start is where it stops
- offset_start = offset_start + chunk_size
- # Add the last chunk
- all_offsets.append((offset_start, total_size))
-
- # Launch all process (Results is a list of list)
- results = pool.starmap(prod_recomb, all_offsets)
+ try:
+ # Create the pool of process
+ pool = Pool()
+ # Partial function to fix all but firsts arguments
+ prod_recomb=partial(get_recombinations, file=file, k=k, gap=gap,
+ graph1=graph1, graph2=graph2)
+ # All tuples of offset_start, offset_end
+ all_offsets = []
+ # For each thread/chunk
+ for _ in range(nb_proc - 1):
+ # Compute the ending offset for this chunk
+ offset_end = offset_start + chunk_size
+ # Add this couple of start/end
+ all_offsets.append((offset_start, offset_end))
+ # Next start is where it stops
+ offset_start = offset_start + chunk_size
+ # Add the last chunk
+ all_offsets.append((offset_start, total_size))
+
+ # Launch all process (Results is a list of list)
+ results = pool.starmap(prod_recomb, all_offsets)
+ except ValueError as exc:
+ print(exc)
+ pool.terminate()
+ sys.exit(1)
+ pool.terminate()
# Get a flatten list
all_queries = []
diff --git a/tests/test_core.py b/tests/test_core.py
index 02296aad258da5b54b7f5b8aa12f5072fae6b9ca..7d371861cba77328e453a74b128cebfdf750029e 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -144,14 +144,13 @@ def test_next_read(capsys, tmpdir):
fastqgz_file = tmpdir.join("test.fastq.gz")
with gzip.open(fastqgz_file, "wb") as fil:
fil.write(data)
- with pytest.raises(SystemExit) as pytest_wrapped_e:
+ with pytest.raises(ValueError) as pytest_wrapped_e:
res = core.next_read(fastqgz_file, 0, 35)
a_read = next(res)
- assert pytest_wrapped_e.type == SystemExit
- assert pytest_wrapped_e.value.code == 1
- captured = capsys.readouterr()
- assert "File error: enable to understand type of file {} "\
- "(+)".format(fastqgz_file) in captured.out
+ assert pytest_wrapped_e.type == ValueError
+ assert str(pytest_wrapped_e.value) == "File error: enable to understand "\
+ "type of file {} "\
+ "(+)".format(fastqgz_file)
def test_build_graph(capsys):
""" Test function 'build_graph(ref, k)'"""
@@ -243,6 +242,37 @@ def test_get_recombinations(tmpdir):
assert all_queries[1].matches[0].__repr__() == "(1, 0, 11, 3, 14, 11, [0]"\
", 2)"
+ """ Test function 'get_recombinations(offset_start, offset_end,
+ file, k, gap, graph1,
+ graph2=None)'"""
+ # Fake false input file
+ file = tmpdir.join("test.fasta")
+ file.write("?Fake1\nACGTTATATGTTGATTAGCTGA\nTGTG\n>Fake2\nCAGTACTAGCAGGTA"\
+ "TGCTAGA")
+ # Fake ref
+ ref = "AAACGACGTTATATGTCGATTAGCTGAAAC"
+ # Fake second ref
+ ref2 = "TTTTGCTAGTACTGTTT"
+ # Gap size
+ gap = 1
+ # Kmer size
+ k = 10
+ # Read the whole file
+ offset_start = 0
+ offset_end = 1000
+ # Build graphs
+ graph1 = core.build_graph(ref, k)
+ graph2 = core.build_graph(ref2, k)
+ # Get the queries
+ with pytest.raises(ValueError) as pytest_wrapped_e:
+ all_queries = core.get_recombinations(offset_start, offset_end, file,
+ k, gap, graph1, graph2)
+ # We have a ValueError
+ assert pytest_wrapped_e.type == ValueError
+ assert str(pytest_wrapped_e.value) == "File error: enable to understand "\
+ "type of file {} "\
+ "(?)".format(file)
+
def test_get_all_queries(tmpdir):
""" Test function 'get_all_queries(file, nb_proc, k, gap, graph1,
graph2=None)'"""
diff --git a/tests/test_functional.py b/tests/test_functional.py
index 1b354c9524ff388130779d65bf5be48d0a4f5e48..3a337fe79ebbd515c1bc6dc1bdfb0250683b7f40 100644
--- a/tests/test_functional.py
+++ b/tests/test_functional.py
@@ -1,13 +1,14 @@
"""Functional tests for FRAG.py"""
import os
+import pytest
import unittest.mock
from collections import defaultdict
from shutil import copyfile
from frags import FindRecombinationsAmongGenomes
from .context import frags
-def test_main(tmpdir):
+def test_main(tmpdir, capsys):
""" Test the functional behavior of FRAG """
# Output folder
@@ -264,6 +265,81 @@ def test_main(tmpdir):
"(+)(1)0:39|(+)(2)74:37|(+)(2)152:43\t(1)1792:39|(2)268:37|"\
"(2)607:43\t39|37|43\t0|0|0\t1|2\n")
+ # Input fastq file to analyze with error
+ false_file = tmpdir.join("false_functional_tests.fastq")
+ false_file.write("@10_insertions_in_contiguous_read\n"\
+ "ATGGTGCGAAGAGTCTATTGAGCTAATTGGTAGTCCTCCGGCCAAACCCTTTGCCTGAA"\
+ "TGCGGCTAATCCCAACTGCGGAGCAGATACCCACATGCCAGTGGGCAGTCT\n"\
+ "+expected_results_A.csv\n"\
+ "10_insertions_in_contiguous_read\t0\t0\tNone\t(+)(1)0:110\t"\
+ "(1)413:110\t110\t10\tNone\n"\
+ "?11_insertions_in_contiguous_read\n"\
+ "ATGGTGCGAAGAGTCTATTGAGCTAATTGGTAGTCCTCCGGCCAAACCCTTTGGCCTGA"\
+ "ATGCGGCTAATCCCAACTGCGGAGCAGATACCCACATGCCAGTGGGCAGTCT\n"\
+ "+expected_results_A.csv\n"\
+ "11_insertions_in_contiguous_read\t0\t1\t43:11\t(+)(1)0:43|"\
+ "(+)(1)54:57\t(1)413:43|(1)456:57\t43|57\t0|0\tNone\n"\
+ "@A_then_2_B_in_rc\n"\
+ "TGTGAACAAGGTGTGAAGGCATCGCCGTGTTCGACGGCAACCAACGCAGCCTGGACCAC"\
+ "CGTCGCCGGTGGGGAACACAGACTTACGCGTTACGACAGGCTAATTGCTGGATTGC\n"\
+ "+expected_results_A_and_B.csv\n"\
+ "A_then_2_B_in_rc\t2\t2\t40:0|75:0\t(+)(1)0:40|(-)(2)40:35|"\
+ "(-)(2)75:40\t(1)1126:40|(2)336:35|(2)495:40\t40|35|40\t"\
+ "0|0|0\tNone\n"\
+ "@Nothing\n"\
+ "AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGAGAGAGAGAGAGAGAGA\n"\
+ "+expected_results_unmatched.csv\n"\
+ "Nothing\n"
+ "@A_then_Blast_then_B_then_Blast_then_B\n"\
+ "ATCACTTTGATGGGTATAAACAACAAGCGGTAGTGATTAACAAGAGGAGCAAGAACAAC"\
+ "ATCAAGAGTCAGGGCTGGAATCTTCGATGCGTTGCGCTCAGCACTCAACCCCCTTCTTA"\
+ "TTGTCATAACAGTGGTATCTGACTCCCACCTTCAATTGTTATCATAAAGCGAGTTGGAT"\
+ "TGGCCATCCAGTGAGAAT\n"\
+ "+expected_results_A_and_B.csv\n"\
+ "A_then_Blast_then_B_then_Blast_then_B\t0\t2\t39:35|111:41\t"\
+ "(+)(1)0:39|(+)(2)74:37|(+)(2)152:43\t(1)1792:39|(2)268:37|"\
+ "(2)607:43\t39|37|43\t0|0|0\t1|2\n")
+
+ # Input fastq file to analyze with error
+ false_fasta_file = tmpdir.join("false_functional_tests.fasta")
+ false_fasta_file.write("?10_insertions_in_contiguous_read\n"\
+ "ATGGTGCGAAGAGTCTATTGAGCTAATTGGTAGTCCTCCGGCCAAACCCTTTGCCTGAA"\
+ "TGCGGCTAATCCCAACTGCGGAGCAGATACCCACATGCCAGTGGGCAGTCT\n"\
+ "?11_insertions_in_contiguous_read\n"\
+ "ATGGTGCGAAGAGTCTATTGAGCTAATTGGTAGTCCTCCGGCCAAACCCTTTGGCCTGA"\
+ "ATGCGGCTAATCCCAACTGCGGAGCAGATACCCACATGCCAGTGGGCAGTCT\n"\
+ ">A_then_2_B_in_rc\n"\
+ "TGTGAACAAGGTGTGAAGGCATCGCCGTGTTCGACGGCAACCAACGCAGCCTGGACCAC"\
+ "CGTCGCCGGTGGGGAACACAGACTTACGCGTTACGACAGGCTAATTGCTGGATTGC\n"\
+ ">A_then_Blast_then_B_then_Blast_then_B\n"\
+ "ATCACTTTGATGGGTATAAACAACAAGCGGTAGTGATTAACAAGAGGAGCAAGAACAAC"\
+ "ATCAAGAGTCAGGGCTGGAATCTTCGATGCGTTGCGCTCAGCACTCAACCCCCTTCTTA"\
+ "TTGTCATAACAGTGGTATCTGACTCCCACCTTCAATTGTTATCATAAAGCGAGTTGGAT"\
+ "TGGCCATCCAGTGAGAAT\n")
+
+ # Try the full software with wrong fastq file
+ with unittest.mock.patch("sys.argv", ["func_test", "-i", str(false_file),
+ "-r", str(ref_a), str(ref_b),
+ "-o", str(output_folder), "-k", "30",
+ "-m", "10", "-p", "4", "-b", "-t",
+ str(h_file)]):
+ assert FindRecombinationsAmongGenomes.main() is None
+
+ # Try the full software with wrong fasta file
+ with pytest.raises(SystemExit) as pytest_wrapped_e:
+ with unittest.mock.patch("sys.argv", ["func_test", "-i",
+ str(false_fasta_file),
+ "-r", str(ref_a), str(ref_b),
+ "-o", str(output_folder), "-k",
+ "30", "-m", "10", "-p", "4",
+ "-b", "-t", str(h_file)]):
+ FindRecombinationsAmongGenomes.main()
+ assert pytest_wrapped_e.type == SystemExit
+ # Error output
+ captured = capsys.readouterr()
+ assert "File error: enable to understand type of file {} "\
+ "(?)".format(false_fasta_file) in captured.out
+
# Try the full software
with unittest.mock.patch("sys.argv", ["func_test", "-i", str(f_file),
"-r", str(ref_a), str(ref_b),